BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124908.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 4,824,708 number of mapped reads = 4,758,317 (98.62%) number of supplementary alignments = 28,052 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,380,806 number of mapped paired reads (second in pair) = 2,377,511 number of mapped paired reads (both in pair) = 4,736,634 number of mapped paired reads (singletons) = 21,683 number of mapped bases = 433,401,204 bp number of sequenced bases = 433,120,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,558 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 100,849.4632 std insert size = 3,038,362.339 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.6584 >>>>>>> ACTG content number of A's = 125,527,021 bp (28.98%) number of C's = 85,341,937 bp (19.7%) number of T's = 127,089,760 bp (29.34%) number of G's = 95,154,699 bp (21.97%) number of N's = 7,309 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 3,604,296 number of insertions = 81,254 mapped reads with insertion percentage = 1.66% number of deletions = 158,534 mapped reads with deletion percentage = 3.26% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.14X std coverageData = 1.7046X There is a 9.12% of reference with a coverageData >= 1X There is a 2.84% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 38985652 0.15641145383545504 1.6722606251616194 chr2 243199373 32026047 0.13168638802370597 1.9578690834159764 chr3 198022430 38894496 0.19641459808366155 0.6633807073442272 chr4 191154276 27891090 0.14590879463245698 1.2116386309976346 chr5 180915260 25130576 0.13890799482586488 0.5025423815667254 chr6 171115067 24143912 0.14109752240578557 1.9654613172511513 chr7 159138663 24135010 0.15166025367449518 1.9643027042021444 chr8 146364022 29478660 0.20140646312657354 0.7795130847212044 chr9 141213431 17874233 0.1265760124474279 2.180591213038074 chr10 135534747 18108247 0.1336059379665939 4.3954072701276194 chr11 135006516 20912644 0.15490099751926048 1.4297890836866722 chr12 133851895 16674436 0.12457377611277001 0.46302672563368674 chr13 115169878 11348935 0.09854082679500624 0.4167705981976721 chr14 107349540 13849516 0.12901327756038825 0.5532928696914966 chr15 102531392 7450819 0.07266866132081773 0.34329727630027007 chr16 90354753 13360481 0.14786694176453563 2.8036508579331603 chr17 81195210 9196305 0.11326166900732199 1.1617076610926893 chr18 78077248 14507183 0.18580551148524088 2.402751576183479 chr19 59128983 10416321 0.17616269503569848 1.1305959954180662 chr20 63025520 9743262 0.15459233021798155 0.6030180539653894 chr21 48129895 5317731 0.11048706838026554 0.6616514815538072 chr22 51304566 4166414 0.08120941906028403 0.4076261195971039 chrMT 16571 142176 8.579808098485305 5.071233479505464 chrX 155270560 12956133 0.08344230226257959 0.7327317641039817 chrY 59373566 6690925 0.1126919848472635 2.7292867565195142